Align Tryptophan-specific transport protein; Tryptophan permease (characterized)
to candidate 208824 DVU3297 tryptophan-specific transport protein
Query= SwissProt::Q02DS7 (417 letters) >MicrobesOnline__882:208824 Length = 419 Score = 417 bits (1071), Expect = e-121 Identities = 214/413 (51%), Positives = 283/413 (68%), Gaps = 1/413 (0%) Query: 5 PAQTPSRRPSLLGGSMIIAGTAVGAGMFSLPIAMSGIWFGWSVAVFLLTWFCMLLSGMMI 64 P Q + RP + GG+MIIAGT++GAGM +LP +G+WFGWS+AV LL W MLLS + Sbjct: 8 PGQNAAHRPGVFGGTMIIAGTSIGAGMLALPTISAGMWFGWSLAVMLLAWLVMLLSSQAL 67 Query: 65 LEANLNYPVGSSFSTITRDLLGQGWNVVNGLSIAFVLYILTYAYISGGGSIIGYTLSSGL 124 LE NL++ G+SF T+ R+ LG GW+V+NG ++AFVLYIL YAY+SGGGSI+ +TL + Sbjct: 68 LEVNLHFEPGASFHTLVRETLGPGWSVINGAAVAFVLYILVYAYVSGGGSIMRHTLLAVS 127 Query: 125 GVTLPEKLAGLLFALAVALVVWWSTRAVDRITTLMLGGMIITFGLSISGLLGRIQPAILF 184 G + AGL FAL +A VWWST VDR++ +M+GGM+++F LS+SG+L I+ +LF Sbjct: 128 GYEPSKLAAGLSFALLLAACVWWSTWIVDRLSVIMMGGMVVSFILSMSGMLSDIRADVLF 187 Query: 185 NSGEPDAVYWPYLLATLPFCLTSFGYHGNVPSLMKYYGKDPQRISRSLWIGTLIALAIYL 244 ++G ++ L LTSF +H +VPSL+KY+G+ P I+R L GT IAL YL Sbjct: 188 DAGGEGGSAL-FVWGALSTYLTSFCFHASVPSLVKYFGRRPADINRCLVGGTGIALVCYL 246 Query: 245 LWQASTLGTIPREQFKGIIAGGSNVGTLVEYLHRITASDSLNALLTTFSNLAVASSFLGV 304 LW + GTIPR +F+ +IA G NVG LV S + +L FS LAVA+SFLG Sbjct: 247 LWIVACDGTIPRAEFRDVIAAGGNVGDLVRAAGSNLNSGFILRMLEAFSALAVATSFLGA 306 Query: 305 TLGLFDYLADLCRFDDSHFGRFKTALLTFVPPTIGGLLFPNGFIYAIGFAGLAAAFWAVI 364 LGLFDY+ADLCRFDD+ GR KT L+TF PPT+GGLL+P+GF+ AIG+AGLAA W+V+ Sbjct: 307 GLGLFDYIADLCRFDDTRAGRTKTTLVTFGPPTVGGLLWPDGFLLAIGWAGLAATVWSVV 366 Query: 365 VPALMARASRKRFGSPLFRAWGGTPAIVLVLLFGVANAVAHILASLHWLPEYR 417 VPALM RASR +P +R GG+ + +L FG+ AV H L LP YR Sbjct: 367 VPALMLRASRATRPAPGYRVGGGSLTVPALLAFGLVTAVCHTLFVFGVLPMYR 419 Lambda K H 0.326 0.141 0.445 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 667 Number of extensions: 29 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 417 Length of database: 419 Length adjustment: 32 Effective length of query: 385 Effective length of database: 387 Effective search space: 148995 Effective search space used: 148995 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory